haplo.stats v1.7.9

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by Jason Sinnwell View Source

Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous

Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.

Functions in haplo.stats

Name	Description
geno.count.pairs	Counts of Total Haplotype Pairs Produced by Genotypes
get.hapPair	Get a list of objects for haplotype pairs
hapPower.demo	Set of haplotypes and frequencies for power and sample size calculations
haplo.hash	Integer Rank Codes for Haplotypes
haplo.scan	Search for a trait-locus by sliding a fixed-width window over each marker locus and scanning all possible haplotype lengths within the window
haplo.em.fitter	Compute engine for haplotype EM algorithm
summary.haplo.glm	Print and summary of a haplo.glm object
anova.haplo.glm	Analysis of variance for haplo.glm model fit
Ginv	Compute Generalized Inverse of Input Matrix
haplo.glm	GLM Regression of Trait on Ambiguous Haplotypes
haplo.model.frame	Sets up a model frame for haplo.glm
haplo.score.merge	Merge haplo.score And haplo.group Objects
haplo.score	Score Statistics for Association of Traits with Haplotypes
haplo.score.slide	Score Statistics for Association of Traits with Haplotypes
print.haplo.em	Print contents of a haplo.em object
find.haplo.beta.qt	Find beta coefficients for risk haplotypes, for specified r2
print.haplo.scan	Print a haplo.scan object
print.haplo.group	Print a haplo.group object
fitted.haplo.glm	Fitted values from haplo.glm fit
chisq.power	Power and sample size for the chi-square distribution
printBanner	Print a nice banner
haplo.design	Build a design matrix for haplotypes
haplo.cc	Haplotype Association Analysis in a Case-Control design
f.power	Power and sample size for the F distribution
haplo.group	Frequencies for Haplotypes by Grouping Variable
haplo.glm.control	Create list of control parameters for haplo.glm
print.haplo.score	Print a haplo.score object
residuals.haplo.glm	Accessing residuals for haplo.glm fit
dglm.fit	Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions.
hla.demo	HLA Loci and Serologic Response to Measles Vaccination
locator.haplo	Find Location from Mouse Clicks and Print Haplotypes on Plot
setupGeno	Create a group of locus objects from a genotype matrix, assign to 'model.matrix' class.
locus	Creates an object of class "locus"
plot.haplo.score	Plot Haplotype Frequencies versus Haplotype Score Statistics
seqhap.dat	Simulated data for seqhap examples
louis.info	Louis Information for haplo.glm
plot.haplo.score.slide	Plot a haplo.score.slide Object
score.sim.control	Create the list of control parameters for simulations in haplo.score
x.sexcheck	consistency checks for x.linked locus
na.geno.keep	Remove rows with NA in covariates, but keep genotypes with NAs
seqhap	Sequential Haplotype Scan Association Analysis for Case-Control Data
print.haplo.score.merge	Print a haplo.score.merge object
print.haplo.score.slide	Print the contents of a haplo.score.slide object
summaryGeno	Summarize Full Haplotype Enumeration on Genotype Matrix
vcov.haplo.glm	variance-covariance matrix of a fitted haplo.glm object
plot.seqhap	Plot a seqhap object
print.haplo.cc	Print a haplo.cc object
summary.haplo.em	Summarize contents of a haplo.em object
geno1to2	convert genotype matrix from 1-column 2-column
haplo.em	EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci
haplo.em.control	Create the Control Parameters for the EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci
haplo.power.qt	Compute either power or sample size for haplotype associations with a quantitative trait.
haplo.power.cc	Compute either power or sample size for haplotype associations in a case-control study.
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Vignettes of haplo.stats

Name
manualHaploStats.pdf.asis
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Details

Date	2018-04-10
License	GPL (>= 2)
VignetteBuilder	R.rsp
URL	http://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software
NeedsCompilation	yes
Packaged	2018-04-11 13:18:13 UTC; sinnwell
Repository	CRAN
Date/Publication	2018-04-11 14:13:58 UTC

depends	graphics , methods , R (>= 3.0.0) , stats
suggests	R.rsp
imports	rms
Contributors	Sinnwell JP, Schaid DJ